Setup

FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
FCC21WPACXX-CHKPEI13070002_L6_1.fq.gz 67,032,866 0 70-100 55
FCC21WPACXX-CHKPEI13070002_L6_2.fq.gz 67,032,866 0 70-100 55
FCC21WPACXX-CHKPEI13070003_L7_1.fq.gz 63,542,676 0 70-100 55
FCC21WPACXX-CHKPEI13070003_L7_2.fq.gz 63,542,676 0 70-100 56
FCC229TACXX-CHKPEI13070001_L3_1.fq.gz 55,762,854 0 70-100 54
FCC229TACXX-CHKPEI13070001_L3_2.fq.gz 55,762,854 0 70-100 55
FCC2GPDACXX-CHKPEI13070004_L2_1.fq.gz 76,201,274 0 70-100 55
FCC2GPDACXX-CHKPEI13070004_L2_2.fq.gz 76,201,274 0 70-100 55
FCC2GPDACXX-CHKPEI13070005_L3_1.fq.gz 76,021,945 0 70-100 55
FCC2GPDACXX-CHKPEI13070005_L3_2.fq.gz 76,021,945 0 70-100 55
FCC2GPDACXX-CHKPEI13070006_L4_1.fq.gz 68,811,191 0 70-100 55
FCC2GPDACXX-CHKPEI13070006_L4_2.fq.gz 68,811,191 0 70-100 55
FCC2GPDACXX-CHKPEI13070007_L6_1.fq.gz 64,940,945 0 70-100 55
FCC2GPDACXX-CHKPEI13070007_L6_2.fq.gz 64,940,945 0 70-100 56

Read Totals

Library Sizes ranged between 55,762,854 and 76,201,274 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Mmusculus Genome

GC Content Distributions for all reads showing theoretical GC content from the Mmusculus Genome

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented Summary

Total overrepresented sequences for each library

Overrepresented Sequences

## The Overrepresented_sequences module was empty in FCC21WPACXX-CHKPEI13070002_L6_1_fastqc.zip
## The Overrepresented_sequences module was empty in FCC21WPACXX-CHKPEI13070003_L7_1_fastqc.zip
## The Overrepresented_sequences module was empty in FCC21WPACXX-CHKPEI13070003_L7_2_fastqc.zip
## The Overrepresented_sequences module was empty in FCC229TACXX-CHKPEI13070001_L3_1_fastqc.zip
## The Overrepresented_sequences module was empty in FCC2GPDACXX-CHKPEI13070004_L2_1_fastqc.zip
## The Overrepresented_sequences module was empty in FCC2GPDACXX-CHKPEI13070005_L3_1_fastqc.zip
## The Overrepresented_sequences module was empty in FCC2GPDACXX-CHKPEI13070006_L4_1_fastqc.zip
## The Overrepresented_sequences module was empty in FCC2GPDACXX-CHKPEI13070007_L6_1_fastqc.zip
Summary of Overrepresented Sequences in all files. A maximum of 9 seqences are shown.
Sequence Total Present In Overall Percentage Max_Percentage Possible_Source
TGCAGGTCACCGAAGATAGGCACGAACCAACACTAATAAGTCTCCCCCAC 1,593,574 5 0.169% 0.692% No Hit
TGCAGGTGTTTACAAAACCTATCAGGCAAACCGAATCCAAGCCTTCTCAT 779,838 5 0.083% 0.306% No Hit
TGCAGGTCACCGAAGATAGGCACAAACCAACACTAATAAGTCTCCCCCAC 712,872 5 0.075% 0.309% No Hit
TGCAGGTCACCGAAGACAGGCACGTTATCAACACCAATAAGTCTCCCCAC 304,747 4 0.032% 0.153% No Hit
TGCAGGGGACTTACAAGACCTATCAGGCAAACCGAATCCAAGCCTTCTCA 166,831 2 0.018% 0.148% No Hit
TGCAGTATAGTATTCTAAAGAGTACATATCCCATAATTTCTTTATCCAGT 144,237 2 0.015% 0.116% No Hit
TGNAGGTCACCGAAGATAGGCACGAACCAACACTAATAAGTCTCCCCCAC 94,135 1 0.010% 0.140% No Hit
TGCAGGTCACCGAAGATAGGCACGAATCAACACCAATAAGCCTCCCCACA 76,838 1 0.008% 0.138% No Hit
TGCAGGTGCTTACAAGCCCTACCAATCAGGCAAACCGAATCCAAGCCTTC 58,296 1 0.006% 0.105% No Hit

Adapter Content

Universal Adapter Content

Kmer Content

## The Kmer_Content module was missing from FCC21WPACXX-CHKPEI13070002_L6_1_fastqc.zip
## The Kmer_Content module was missing from FCC21WPACXX-CHKPEI13070002_L6_2_fastqc.zip
## The Kmer_Content module was missing from FCC21WPACXX-CHKPEI13070003_L7_1_fastqc.zip
## The Kmer_Content module was missing from FCC21WPACXX-CHKPEI13070003_L7_2_fastqc.zip
## The Kmer_Content module was missing from FCC229TACXX-CHKPEI13070001_L3_1_fastqc.zip
## The Kmer_Content module was missing from FCC229TACXX-CHKPEI13070001_L3_2_fastqc.zip
## The Kmer_Content module was missing from FCC2GPDACXX-CHKPEI13070004_L2_1_fastqc.zip
## The Kmer_Content module was missing from FCC2GPDACXX-CHKPEI13070004_L2_2_fastqc.zip
## The Kmer_Content module was missing from FCC2GPDACXX-CHKPEI13070005_L3_1_fastqc.zip
## The Kmer_Content module was missing from FCC2GPDACXX-CHKPEI13070005_L3_2_fastqc.zip
## The Kmer_Content module was missing from FCC2GPDACXX-CHKPEI13070006_L4_1_fastqc.zip
## The Kmer_Content module was missing from FCC2GPDACXX-CHKPEI13070006_L4_2_fastqc.zip
## The Kmer_Content module was missing from FCC2GPDACXX-CHKPEI13070007_L6_1_fastqc.zip
## The Kmer_Content module was missing from FCC2GPDACXX-CHKPEI13070007_L6_2_fastqc.zip
## No Kmers were detected by FastQC